bool IDEvaluationBase::addSearchFile(const String& file_name)
{
MSSpectrum<> points;
if (!loadCurve(file_name, points)) return false;
data_.addSpectrum(points);
MSExperiment<>* exp = new MSExperiment<>();
exp->addSpectrum(points);
spec_1d_->canvas()->addLayer(SpectrumCanvas::ExperimentSharedPtrType(exp));
spec_1d_->canvas()->setLayerName(spec_1d_->canvas()->getLayerCount() - 1, points.getMetaValue("search_engine"));
// set intensity mode (after spectrum has been added!)
setIntensityMode((int) SpectrumCanvas::IM_SNAP);
return true;
}
ExitCodes main_(int, const char**)
{
//----------------------------------------------------------------
// load data
//----------------------------------------------------------------
StringList in_list = getStringList_("in");
String out = getStringOption_("out");
String out_csv = getStringOption_("out_csv");
String format = getStringOption_("out_type");
if (out.empty() && out_csv.empty())
{
LOG_ERROR << "Neither 'out' nor 'out_csv' were provided. Please assign at least one of them." << std::endl;
return ILLEGAL_PARAMETERS;
}
if (!out.empty() && format == "") // get from filename
{
try
{
format = out.suffix('.');
}
catch (Exception::ElementNotFound& /*e*/)
{
format = "nosuffix";
}
// check if format is valid:
if (!ListUtils::contains(out_formats_, format.toLower()))
{
LOG_ERROR << "No explicit image output format was provided via 'out_type', and the suffix ('" << format << "') does not resemble a valid type. Please fix one of them." << std::endl;
return ILLEGAL_PARAMETERS;
}
}
double q_min = getDoubleOption_("q_min");
double q_max = getDoubleOption_("q_max");
if (q_min >= q_max)
{
LOG_ERROR << "The parameter 'q_min' must be smaller than 'q_max'. Quitting..." << std::endl;
return ILLEGAL_PARAMETERS;
}
IDEvaluationBase* mw = new IDEvaluationBase();
Param alg_param = mw->getParameters();
alg_param.insert("", getParam_().copy("algorithm:", true));
mw->setParameters(alg_param);
if (!mw->loadFiles(in_list))
{
LOG_ERROR << "Tool failed. See above." << std::endl;
return INCOMPATIBLE_INPUT_DATA;
}
mw->setVisibleArea(q_min, q_max);
if (!out.empty()) // save as image and exit
{
String error;
bool r = mw->exportAsImage(out.toQString(), error, format.toQString());
if (r) return EXECUTION_OK;
else
{
LOG_ERROR << error << std::endl;
return ILLEGAL_PARAMETERS;
}
}
if (!out_csv.empty())
{
TextFile tf;
for (Size i = 0; i < mw->getPoints().size(); ++i)
{
MSSpectrum s = mw->getPoints()[i];
StringList sl1;
StringList sl2;
for (Size j = 0; j < s.size(); ++j)
{
sl1.push_back(s[j].getMZ());
sl2.push_back(s[j].getIntensity());
}
tf.addLine(String("# ") + String(s.getMetaValue("search_engine")));
tf.addLine(ListUtils::concatenate(sl1, ","));
tf.addLine(ListUtils::concatenate(sl2, ","));
}
tf.store(out_csv);
}
delete(mw);
return EXECUTION_OK;
}
tmp.getInstrumentSettings().getScanWindows().resize(1);
tmp.setMetaValue("label",5.0);
tmp.setMSLevel(17);
tmp.setRT(7.0);
tmp.setDriftTime(8.0);
tmp.setName("bla");
//peaks
MSSpectrum::PeakType peak;
peak.getPosition()[0] = 47.11;
tmp.push_back(peak);
//normal assignment
MSSpectrum tmp2;
tmp2 = tmp;
TEST_EQUAL(tmp2.getInstrumentSettings().getScanWindows().size(),1);
TEST_REAL_SIMILAR(tmp2.getMetaValue("label"), 5.0)
TEST_EQUAL(tmp2.getMSLevel(), 17)
TEST_REAL_SIMILAR(tmp2.getRT(), 7.0)
TEST_REAL_SIMILAR(tmp2.getDriftTime(), 8.0)
TEST_EQUAL(tmp2.getName(),"bla")
TEST_EQUAL(tmp2.size(),1);
TEST_REAL_SIMILAR(tmp2[0].getPosition()[0],47.11);
//Assignment of empty object
//normal assignment
tmp2 = MSSpectrum();
TEST_EQUAL(tmp2.getInstrumentSettings().getScanWindows().size(),0);
TEST_EQUAL(tmp2.metaValueExists("label"), false)
TEST_EQUAL(tmp2.getMSLevel(),1)
TEST_REAL_SIMILAR(tmp2.getRT(), -1.0)
TEST_REAL_SIMILAR(tmp2.getDriftTime(), -1.0)